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PR - Big book > 11.1-11.7 DNA replication, translation > Flashcards

11.1-11.7 DNA replication, translation Flashcards

1
Q

intergenic space

A

noncoding DNA

human has 3.2 billion BPs, 21,000 genes, and long stretches of intergenic regions (noncoding DNA) which may direct chromatin structure / regulate genes / no known function

include TANDEM REPEATS and TRANSPOSONS

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2
Q

gene

A

codes for gene product

includes REGULATORY sites (promoters, transcription stop sites), and “ACTIVE” site (codes for protein or non-coding RNA)

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3
Q

single nucleotide polymorphism

A

ALLELE - 1 nucleotide change once every 1000 bp’s, “snips” are essentially mutations

  • > sickle-cell anemia, beta-thalassemia, cystic fibrosis
  • > see picture
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4
Q

copy number variation

A

structural variations in genome (large regions of genome 10^3-10^6 can be duplicated)

DUPLICATION OF DNA, or DELETED

5-10% of human genome

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5
Q

Tandem repeats

A

short sequence of nucleotides repeat right after each other, 3-100 times

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6
Q

Transposons

A

genes code for tranposase (“cut and paste” activity)

“jumping” around the genome; very mischievous

CAUSES or REVERSES mutations

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7
Q

Hershey and Chase

A

proved DNA is the genetic material

Watch video

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8
Q

ribosome

A

very large, rRNA and protein

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9
Q

UGA

A

university of georgia at atlanta (stop codon)

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10
Q

topoisomerase

A

cuts strand and unwraps helix, releasing excess TENSION

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11
Q

single-strand binding protein

A

proteins DNA that has been de-doubled-stranded (much less stable), leads to the OPEN COMPLEX (ready to begin replication)

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12
Q

Initiation-open complex

A

an RNA primer MUST be synthesized for each template strand – primosome (contains RNA polymerase primase)

DNA pol CANNOT START a DNA chain from scratch. The RNA primer is 8-12 nucleotides long, later replaced by DNA

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13
Q

DNA Pol

A

part of a larger complex of proteins called the REPLISOME

prokaryote - 13 components
eukaryote - 27 proteins

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14
Q

thermo of DNA replication

A

removal and hydrolysis of pryophosphate (two phosphates) from each dTNP (dTNP is the nucleotide with 3 phosphates)

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15
Q

Okazaki fragments are joined by

A

DNA ligase

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16
Q

prokaryotic DNA polymerases (III and I)

A

I, II, III, and IV

III - elongation of leading strand; has 5-3 polymerase and 3-5 exonuclease activity; FAST

I - adds nucleotides at the RNA primer, 5-3 polymerase activity, only adds 15-20 nucleotides a second, taken over by pol III 400 bps downstream; capable of 3-5 exonuclease activity; removes the primer via 5-3 exonuclease activity; important for excision repair

II - backup for III

IV and V - error-prone in 5-3 polymerase activity , function to stall other polymerase enzymes at replication forks

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17
Q

telomerase

A

RIBONUCLEOPROTEIN: adds repetitive nucleotides to ends of chromosomes

expressed only in germ line, stem cells, and some white blood cells

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18
Q

transition/transversion

A

substitute pyrimidines for a pyrimidine, purine for a purine

transversion is more severe

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19
Q

translocation

A

common in cancers

two regions swap locations

occurs in genetic recombination

produces a new gene product

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20
Q

loss of heterozygosity

A

one allele of a certain gene is lost, due to deletion or recombination

hemizygous - only 1 gene copy.

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21
Q

direct reversal of dna repair

A

bacteria and plants can repair UV-induced pyrimidine photodimers DIRECTLY

nucleotide excision repair is the next step

main mechanism of repair in humans, but can introduce a mutation

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22
Q

homology-dependency repair

A

DNA is redundant (two copies)

excision repair (before DNA replication) and post-replication repair (after DNA replication)

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23
Q

excision repair

A

BEFORE dna replication; removes defective base and replaces them

24
Q

post-replication repair

A

MMR - mismatch repair pathway - targets mistakes not repaired by DNA polymerase proofreading

DURING dna replication; methylation helps determine which is wrong (A or G)

during replication, the free 3’ end and Okazaki fragments are found

25
homologous recombination to repair DS breaks (see illustration p. 222)
nuclease and helicase generate single-stranded DNA they find complementary sister chromatid dna pol and ligase build new DNA
26
non-homologous recombination repair of DS break
not perfect
27
Open-reading frame (ORF)
after the 5-3 UTR (untranslated region - initiation and regulation), ORF is start to stop codon (coding region)
28
monocistronic v. polycistronic
"one mRNA, one protein" - eukaryotes polycistronic - one mRNA, multiple proteins - prokaryotes; translation can start in multiple places! termination and initiation sequences between each ORF NOTE; PROKARYOTES DON'T PROCESS mRNA, only eukaryotes have hnRNA (which are modified: addition of cap and tail, splicing)
29
rRNA (4 types)
18S, 5.8S, 28S, and 5S serve in ribosome - along with polypeptide chains (proteins), 1 rRNA provides catalytic function of the ribosome (a RIBOZYME)
30
Driving force of replication/transcription
removal and hydrolysis of pyrophosphate from each nucleotide added
31
promotor (transcription) versus start site
the area of DNA that ACTIVATES transcription (origin is where DNA is replicated) START site is called the "START SITE"
32
antisense and sense strands
the DNA template is the antisense (because it's the ANTI of the mRNA) coding strand ("sense"); +1 is the first nucleotide transcribed mRNA grows on the 3' end -> proceeds downstream
33
RNA polymerase
pribnow box (-10) and -35 sequence forms a CLOSED COMPLEX RNA pol must unwind DNA RNA pol HOLOenzyme bound at promotor with a region of single-stranded DNA is termed the OPEN COMPLEX (difference is that the DNA is unwound)
34
bacteria transcription
All RNA is made of the same RNA pol a large enzyme - 5 subunits Core enzyme - rapid elongation Subunit sigma factor (forms the HOLO-enzyme) - responsible for initiation Initiation -> elongation -> termination
35
sigma factor
helps prokaryotes find promoters
36
processive elogation
core enzyme moves along the DNA downstream, a bubble forms when the DNA is unwound rho helps determine when to end, polymerase falls off and bubble is closed
37
eukaryotes location of transcription
nucleus modify in the nucleus, transport to cytoplasm where it is translated
38
prokaryotes translate...
...while transcribing, no post-processing involved
39
eukaryotic splicing
extensive modification after transcription - splicing these non-coding regions (introns) may code for proteins, contain ENHANCERS or REGULATORY sequences
40
spliceosome (and snRNA)
mediates eukaryotic mRNA splicing 100 proteins and 5 small nuclear RNA molecules the snRNA "detects" the intron (see image p. 227) ALTERNATIVE splicing - multiple ways of splicing hnRNA cap and tails must be added (5' cap, and 3' poly-A tail)
41
RNA polymerases
I - rRNa II - hnRNA, most snRNA III - tRNA
42
tRNA, the protein bonds to
the 3' end
43
wobble hypothesis
of anticodon: 3rd position is more flexible than 1 and 2 5' base anticodon (tRNA) - 3' base in codon (mRNA) G -> C or U U -> A or G I -> A, U, C
44
Amino Acid Activation p. 231
Need help understanding this... 1. amino acid attaches to AMP to form aminoacyl AMP 2. pyrophosphate leaving group is hydrolyzed to 2 orthophosphates (delta_G << 0) 3. tRNA loading (deltaG >> 0) - driven by the destruction of the aminoacyl-AMP bond (basically AMP is released fro aminoacyl amp, leading to the aminoacyl-tRNA) Final product: Aminoacyl-tRNA Requires: 2 atp equivalents
45
aminoacyl-tRNA synthetase anzyme
family of enzymes that recognizes the tRNA and amino acid , puts them together -- HIGHLY SPECIFIC
46
prokaryotic ribosome
30S and 50S => 70S 30S -> 16S rRNA and 21 peptides 50S -> 23S and 5S and 31 peptides
47
eukaryotic ribosome
80S ribosome large -> 60S -> 5S, 5.8S, 28S and 46 peptides small -> 40S -> 18S, 33 peptides
48
the 5' end ORF
upstream regulatory sequence is essential for initiation, we have a ribosome binding site (Shine-Dalgarno sequence) located at -10. SD sequence is complementary to a pyrimidine rich region on the small subunit
49
translation has three distinct stages
initiation, elongation, termination
50
initiation
30S binds two initiation proteins called IF1 and IF3, which binds to the mRNA transcript, then aminoacyl-tRNA joins, then IF2, which is bound to 1 GTP. 50S completes the complex Powered by hydrolysis of 1 GTP molecule first aminoacyl-tRNA is called the initiator tRNA (fMet-tRNA) - sits in P site of 70S ribosome, hydrogen-bonded with the start codon
51
elongation
three-steps 1. second aminoacyl-tRNA enters the A site, h-bonds with the second codon (1 GTP) 2. peptidyl transferase activity of large ribosomal subunit (23S) catalyzes formation of a peptide bond between fMet and the second amino acid (driven by hydrolysis of tRNA and amino acid p. 231) 3. translocation - tRNA #1 moves to E site, tRNA #2 (holding the growing peptide) moves to the P site, and next codon moves into the A site. (1 GTP)
52
termination
when stop codon appears in the A site a release factor enters the A site, causes peptidyl transferase to hydrolyze the bond between the last tRNA and completed polypeptide
53
5' UTR
untranslated region - common in eukaryotes (e.g. Kozak sequence), located several nucleotides before start codon
54
eukaryotic transcription begins...
...with formation of initiation complex 43S small ribosomal subunit forms + Met-tRNA_Met + several proteins called eukaryotic initiation factors (eIFs); this is recruited to 5' capped end of transcript, by initiation complex of proteins; additional proteins recruited (polyA tail binding protein) Initiation complex starts scanning the 5' end, looking for a start codon Once found, the large ribosomal subunit (60S) is recruited and translation begins
55
eukaryotes have *** elongation factors
2
56
cap-dependent translation
the mRNA cap, 5' end, is so important for translation but cap-independent translation was discovered site has IRES (ribosome entry site) -> helps apoptosis or deal with stress

PR - Big book (29 decks)

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